The microbiome is the group of genomes of bacteria which colonise an animal's body. They are considered collectively for purely practical reasons. Rather than successively sequence the genomes of all species of bacteria, metagenomics methods are used as they can be applied to an entire ecosystem.
Bacteria that live commensurably in animal bodies play very important roles in them, particularly in digestion and defence against pathogenic organisms.
It is believed that the human body houses more than ten times the number of bacteria as it has cells itself. Together these populations form an ecosystem, about which we know little but it is now being studied.